I really don't care what bike you get from whom, but I would like for you to consider the markup on bikes and the special ordering process.
If a shop has gone through their quota (for lack of a better word for it) and has to special order you the bike you want, then the shop has to pay shipping on one bike and a single wholesale price which is higher than the multiple purchase price. This is true no matter who you shop with.
The way I see it, your choses are as such, buy another brand/model bike, ask the lbs to check for clearance bikes (older models might still be around), suck it up and special order the coda that you want at retail (and know that you are getting a quality bike while being treated fairly), or you can wait for a 2010 model and then try to haggle.
Whatever you do remember that the majority of lbs are independantly owned and do have a certain amount of overhead and not a lot of profit margin. So, its not like buying a car where the margin equals thousands of dollars, but more likely less than $100 in most cases.
Sorry if that seems like a rant, you have no idea how many people I talk to daily that can't fathum a $500+ bicycle. And when you say "that one that you're looking at costs $1k," the reaction is often, "that's as much as a car," "you can get a car for that." etc.
On a side note, guy walks into the shop and wants a 7sp cruiser, I show him Boss cruisers for $425 and he rudly says "Thats too much" and walks away, then turns around and I show him some Sun Drifters at $400, he'll have to think about it and come back he says. But there is only $25 difference in the price and the $399.99 price is ok?